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Community detection can reveal the underlying structure and patterns of complex networks, identify sets of nodes with specific functions or similar characteristics, and study the evolution process and development trends of networks. Despite…
Many active systems are capable of forming intriguing patterns at scales significantly larger than the size of their individual constituents. Cyanobacteria are one of the most ancient and important phyla of organisms that has allowed the…
This paper focuses on two fundamental tasks of graph analysis: community detection and node representation learning, which capture the global and local structures of graphs, respectively. In the current literature, these two tasks are…
Living systems exhibit complex yet organized behavior on multiple spatiotemporal scales. To investigate the nature of multiscale coordination in living systems, one needs a meaningful and systematic way to quantify the complex dynamics, a…
Networks are useful for describing systems of interacting objects, where the nodes represent the objects and the edges represent the interactions between them. The applications include chemical and metabolic systems, food webs as well as…
Complex networks often exhibit co-evolutionary dynamics, meaning that the network topology and the state of nodes or links are coupled, affecting each other in overlapping time scales. We focus on the co-evolutionary dynamics of online…
We consider a finite structured population of mobile individuals that strategically explore a network using a Markov movement model and interact with each other via a public goods game. We extend the model of Erovenko et al. (2019) from…
The rapid evolution of network services demands new paradigms for studying and designing networks. In order to understand the underlying mechanisms that provide network functions, we propose a framework which enables the functional analysis…
The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other elements through the biosphere on a…
We introduce a new method for temporal pattern analysis of scientific collaboration networks. We investigate in particular virus research activities through five epidemic or pandemic outbreaks in the recent two decades and in the ongoing…
Evolutionary models are used to study the self-organisation of collective action, often incorporating population structure due to its ubiquitous presence and long-known impact on emerging phenomena. We investigate the evolution of…
Learning graph convolutional networks (GCNs) is an emerging field which aims at generalizing convolutional operations to arbitrary non-regular domains. In particular, GCNs operating on spatial domains show superior performances compared to…
Functional groups (FGs) are molecular substructures that are served as a foundation for analyzing and predicting chemical properties of molecules. Automatic discovery of FGs will impact various fields of research, including medicinal…
Community structure is of paramount importance for the understanding of complex networks. Consequently, there is a tremendous effort in order to develop efficient community detection algorithms. Unfortunately, the issue of a fair assessment…
Cooperation plays a fundamental role in societal and biological domains, and the population structure profoundly shapes the dynamics of evolution. Practically, individuals behave either altruistically or egoistically in multiple groups,…
Community detection is the task of discovering groups of nodes sharing similar patterns within a network. With recent advancements in deep learning, methods utilizing graph representation learning and deep clustering have shown great…
Graphs can be used to effectively represent complex data structures. Learning these irregular data in graphs is challenging and still suffers from shallow learning. Applying deep learning on graphs has recently showed good performance in…
Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…
Sequence differences between the strains of bacteria comprising host-associated and environmental microbiota may play a role in community assembly and influence the resilience of microbial communities to disturbances. Tools for…
The absence of a conventional association between the cell-cell cohabitation and its emergent dynamics into cliques during development has hindered our understanding of how cell populations proliferate, differentiate, and compete, i.e. the…